.. _`bio/multiqc`:

MULTIQC
=======


.. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/multiqc?label=version%20update%20pull%20requests
   :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/multiqc

Generate qc report using multiqc.


**URL**: https://multiqc.info/

Example
-------

This wrapper can be used in the following way:

.. code-block:: python

    rule multiqc_dir:
        input:
            expand("samtools_stats/{sample}.txt", sample=["a", "b"]),
        output:
            "qc/multiqc.html",
            directory("qc/multiqc_data"),
        params:
            extra="--data-dir",  # Optional: extra parameters for multiqc.
        log:
            "logs/multiqc.log",
        wrapper:
            "v3.0.1/bio/multiqc"


    rule multiqc_file:
        input:
            expand("samtools_stats/{sample}.txt", sample=["a"]),
        output:
            "qc/multiqc.a.html",
            "qc/multiqc.a_data.zip",
        params:
            extra="--zip-data-dir",  # Optional: extra parameters for multiqc.
            use_input_files_only=True,  # Optional, use only a.txt and don't search folder samtools_stats for files
        log:
            "logs/multiqc.log",
        wrapper:
            "v3.0.1/bio/multiqc"

Note that input, output and log file paths can be chosen freely.

When running with

.. code-block:: bash

    snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.


Software dependencies
---------------------

* ``multiqc=1.18``

Input/Output
------------
**Input:**

* input directory containing qc files, default behaviour is to extract folder path from the provided files or parent folder if a folder is provided.

**Output:**

* qc report (html)
* multiqc data folder or zip (optional)



Params
------

* ``use_input_files_only``: if this variable is set to True input will be used as it is, i.e no folder will be extract from provided file names




Authors
-------

* Julian de Ruiter


Code
----

.. code-block:: python

    """Snakemake wrapper for trimming paired-end reads using cutadapt."""

    __author__ = "Julian de Ruiter"
    __copyright__ = "Copyright 2017, Julian de Ruiter"
    __email__ = "julianderuiter@gmail.com"
    __license__ = "MIT"


    import tempfile
    from pathlib import Path
    from snakemake.shell import shell


    extra = snakemake.params.get("extra", "")
    log = snakemake.log_fmt_shell(stdout=True, stderr=True)


    # Set this to False if multiqc should use the actual input directly
    # instead of parsing the folders where the provided files are located
    use_input_files_only = snakemake.params.get("use_input_files_only", False)
    if not use_input_files_only:
        input_data = set(Path(fp).parent for fp in snakemake.input)
    else:
        input_data = set(snakemake.input)


    with tempfile.TemporaryDirectory() as tmpdir:
        shell(
            "multiqc"
            " {extra}"
            " --outdir {tmpdir}"
            " --filename out"
            " {input_data}"
            " {log}"
        )

        for output in snakemake.output:
            if output.endswith("_data"):
                ext = "_data"
            elif output.endswith(".zip"):
                ext = "_data.zip"
            else:
                ext = Path(output).suffix
            shell("mv {tmpdir}/out{ext} {output}")


.. |nl| raw:: html

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